Domain adaptation studies learning algorithms that generalize across source domains and target domains that exhibit different distributions. Recent studies reveal that deep neural networks can learn ...transferable features that generalize well to similar novel tasks. However, as deep features eventually transition from general to specific along the network, feature transferability drops significantly in higher task-specific layers with increasing domain discrepancy. To formally reduce the effects of this discrepancy and enhance feature transferability in task-specific layers, we develop a novel framework for deep adaptation networks that extends deep convolutional neural networks to domain adaptation problems. The framework embeds the deep features of all task-specific layers into reproducing kernel Hilbert spaces (RKHSs) and optimally matches different domain distributions. The deep features are made more transferable by exploiting low-density separation of target-unlabeled data in very deep architectures, while the domain discrepancy is further reduced via the use of multiple kernel learning that enhances the statistical power of kernel embedding matching. The overall framework is cast in a minimax game setting. Extensive empirical evidence shows that the proposed networks yield state-of-the-art results on standard visual domain-adaptation benchmarks.
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in ...downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task.
Accelerated gradient methods play a central role in optimization, achieving optimal rates in many settings. Although many generalizations and extensions of Nesterov’s original acceleration method ...have been proposed, it is not yet clear what is the natural scope of the acceleration concept. In this paper, we study accelerated methods from a continuous-time perspective. We show that there is a Lagrangian functional that we call the Bregman Lagrangian, which generates a large class of accelerated methods in continuous time, including (but not limited to) accelerated gradient descent, its non-Euclidean extension, and accelerated higher-order gradient methods. We show that the continuous-time limit of all of these methods corresponds to traveling the same curve in spacetime at different speeds. From this perspective, Nesterov’s technique and many of its generalizations can be viewed as a systematic way to go from the continuous-time curves generated by the Bregman Lagrangian to a family of discrete-time accelerated algorithms.
Working under a model of privacy in which data remain private even from the statistician, we study the tradeoff between privacy guarantees and the risk of the resulting statistical estimators. We ...develop private versions of classical information-theoretical bounds, in particular those due to Le Cam, Fano, and Assouad. These inequalities allow for a precise characterization of statistical rates under local privacy constraints and the development of provably (minimax) optimal estimation procedures. We provide a treatment of several canonical families of problems: mean estimation and median estimation, generalized linear models, and nonparametric density estimation. For all of these families, we provide lower and upper bounds that match up to constant factors, and exhibit new (optimal) privacy-preserving mechanisms and computationally efficient estimators that achieve the bounds. Additionally, we present a variety of experimental results for estimation problems involving sensitive data, including salaries, censored blog posts and articles, and drug abuse; these experiments demonstrate the importance of deriving optimal procedures. Supplementary materials for this article are available online.
As the number of single‐cell transcriptomics datasets grows, the natural next step is to integrate the accumulating data to achieve a common ontology of cell types and states. However, it is not ...straightforward to compare gene expression levels across datasets and to automatically assign cell type labels in a new dataset based on existing annotations. In this manuscript, we demonstrate that our previously developed method, scVI, provides an effective and fully probabilistic approach for joint representation and analysis of scRNA‐seq data, while accounting for uncertainty caused by biological and measurement noise. We also introduce single‐cell ANnotation using Variational Inference (scANVI), a semi‐supervised variant of scVI designed to leverage existing cell state annotations. We demonstrate that scVI and scANVI compare favorably to state‐of‐the‐art methods for data integration and cell state annotation in terms of accuracy, scalability, and adaptability to challenging settings. In contrast to existing methods, scVI and scANVI integrate multiple datasets with a single generative model that can be directly used for downstream tasks, such as differential expression. Both methods are easily accessible through scvi‐tools.
SYNOPSIS
This study demonstrates the ability of scVI to integrate single‐cell RNA‐seq datasets in a variety of settings and presents scANVI, a new development based on scVI for automated annotation of cell types and states.
In scVI, datasets from different labs and technologies are integrated in a joint latent space.
In scANVI, cell type annotations are transferred between datasets and across different scenarios.
Uncertainties of differential gene expression in multiple samples are quantified.
The performance of scVI and scANVI in data integration and cell state annotation is superior to other related methods.
This study demonstrates the ability of scVI to integrate single‐cell RNA‐seq datasets in a variety of settings and presents scANVI, a new development based on scVI for automated annotation of cell types and states.
We present a communication-efficient surrogate likelihood (CSL) framework for solving distributed statistical inference problems. CSL provides a communication-efficient surrogate to the global ...likelihood that can be used for low-dimensional estimation, high-dimensional regularized estimation, and Bayesian inference. For low-dimensional estimation, CSL provably improves upon naive averaging schemes and facilitates the construction of confidence intervals. For high-dimensional regularized estimation, CSL leads to a minimax-optimal estimator with controlled communication cost. For Bayesian inference, CSL can be used to form a communication-efficient quasi-posterior distribution that converges to the true posterior. This quasi-posterior procedure significantly improves the computational efficiency of Markov chain Monte Carlo (MCMC) algorithms even in a nondistributed setting. We present both theoretical analysis and experiments to explore the properties of the CSL approximation. Supplementary materials for this article are available online.
Gradient-based optimization algorithms can be studied from the perspective of limiting ordinary differential equations (ODEs). Motivated by the fact that existing ODEs do not distinguish between two ...fundamentally different algorithms—Nesterov’s accelerated gradient method for strongly convex functions (NAG-SC) and Polyak’s heavy-ball method—we study an alternative limiting process that yields
high-resolution ODEs
. We show that these ODEs permit a general Lyapunov function framework for the analysis of convergence in both continuous and discrete time. We also show that these ODEs are more accurate surrogates for the underlying algorithms; in particular, they not only distinguish between NAG-SC and Polyak’s heavy-ball method, but they allow the identification of a term that we refer to as “gradient correction” that is present in NAG-SC but not in the heavy-ball method and is responsible for the qualitative difference in convergence of the two methods. We also use the high-resolution ODE framework to study Nesterov’s accelerated gradient method for (non-strongly) convex functions, uncovering a hitherto unknown result—that NAG-C minimizes the squared gradient norm at an inverse cubic rate. Finally, by modifying the high-resolution ODE of NAG-C, we obtain a family of new optimization methods that are shown to maintain the accelerated convergence rates of NAG-C for smooth convex functions.
Extreme precipitation is a considerable contributor to meteorological disasters and there is a great need to mitigate its socioeconomic effects through skilful nowcasting that has high resolution, ...long lead times and local details
. Current methods are subject to blur, dissipation, intensity or location errors, with physics-based numerical methods struggling to capture pivotal chaotic dynamics such as convective initiation
and data-driven learning methods failing to obey intrinsic physical laws such as advective conservation
. We present NowcastNet, a nonlinear nowcasting model for extreme precipitation that unifies physical-evolution schemes and conditional-learning methods into a neural-network framework with end-to-end forecast error optimization. On the basis of radar observations from the USA and China, our model produces physically plausible precipitation nowcasts with sharp multiscale patterns over regions of 2,048 km × 2,048 km and with lead times of up to 3 h. In a systematic evaluation by 62 professional meteorologists from across China, our model ranks first in 71% of cases against the leading methods. NowcastNet provides skilful forecasts at light-to-heavy rain rates, particularly for extreme-precipitation events accompanied by advective or convective processes that were previously considered intractable.
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